The trust’s remaining four academies are still in limbo, a year after it announced plans to give up its schools.

A DfE spokesperson said new trusts for the remaining schools “will be confirmed shortly”, and the sponsorship deals for all 12 schools “will bring about rapid and sustained improvement”.

The trust, which is responsible for the education of around 6,500 children, became the first to announce plans to give up every one of its schools last spring.

Lizzie Howe, its chief operating officer, said at the time the request to transfer its schools was caused by “financial constraints facing the education sector and the misalignment of values with the Department for Education”.

According to the trust’s latest accounts, the DfE initially planned to transfer all 12 schools to new sponsors by the end of 2017. However, the it now estimates the transfers will be complete by July 2018.

These delays “will impact on our finances and result in additional costs including the ongoing legal and financial work”, and will mean additional central funding “which was not budgeted for based on the initial timelines given by the DfE”, the trust said.

The accounts also show that four of the trust’s schools were in deficit as of the end of August 2017. Wrenn Academy in Northamptonshire, which government officials moved to rebroker from the trust in January last year, had a deficit of almost £1.4 million, while Desborough College in Berkshire had a deficit of more than £1.1 million. Clarendon Academy and Pembroke Park Academy in Wiltshire had deficits of £727,000 and £238,000 respectively.

The trust had originally planned to reduce the deficits at all four schools so they could repay loans to the chain’s central funds. At Clarendon Academy, the deficit included “considerable redundancy costs”, but it is expected to break even in 2017-18.

Pembroke Park’s deficit arose from the financial cost of “doubling the physical size of the school”, which went ahead because its local council estimated that pupil numbers would double. But the increase in pupils “has not occurred despite assurances from the local authority”.

Accounts also show that a commercial company linked to the trust remained active last year, despite calls for its closure.

Concerns were raised over the trust’s relationship with the company, which at the time was the chain’s private limited company owner, after the government ruled that the trust’s organisational model was “not acceptable”.

An earlier investigation by the EFA in 2014 also highlighted concerns over governors’ expenses of £45,000, including for a fact-finding trip to New York, and unadvertised jobs that went to family members.